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Beta.java
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Beta.java
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package lphy.base.distribution;
import lphy.core.model.GenerativeDistribution1D;
import lphy.core.model.RandomVariable;
import lphy.core.model.Value;
import lphy.core.model.ValueUtils;
import lphy.core.model.annotation.GeneratorCategory;
import lphy.core.model.annotation.GeneratorInfo;
import lphy.core.model.annotation.ParameterInfo;
import org.apache.commons.math3.distribution.BetaDistribution;
import org.apache.commons.math3.random.RandomGenerator;
import java.util.Map;
import java.util.TreeMap;
import static lphy.base.distribution.DistributionConstants.alphaParamName;
import static lphy.base.distribution.DistributionConstants.betaParamName;
/**
* Beta distribution prior.
* @see BetaDistribution
* @author Alexei Drummond
* @author Walter Xie
*/
public class Beta extends ParametricDistribution<Double> implements GenerativeDistribution1D<Double> {
private Value<Number> alpha;
private Value<Number> beta;
BetaDistribution betaDistribution;
public Beta(@ParameterInfo(name = alphaParamName, description = "the first shape parameter.") Value<Number> alpha,
@ParameterInfo(name = betaParamName, description = "the second shape parameter.") Value<Number> beta) {
super();
this.alpha = alpha;
this.beta = beta;
constructDistribution(random);
}
@Override
protected void constructDistribution(RandomGenerator random) {
// use code available since apache math 3.1
betaDistribution = new BetaDistribution(random, ValueUtils.doubleValue(alpha), ValueUtils.doubleValue(beta),
BetaDistribution.DEFAULT_INVERSE_ABSOLUTE_ACCURACY);
}
@GeneratorInfo(name = "Beta", verbClause = "has", narrativeName = "Beta distribution prior",
category = GeneratorCategory.PRIOR,
examples = {"birthDeathRhoSampling.lphy","simpleBModelTest.lphy"},
description = "The beta probability distribution.")
public RandomVariable<Double> sample() {
// constructDistribution() only required in constructor and setParam
double randomVariable = betaDistribution.sample();
return new RandomVariable<>("x", randomVariable, this);
}
public double logDensity(Double d) {
return betaDistribution.logDensity(d);
}
@Override
public Map<String, Value> getParams() {
return new TreeMap<>() {{
put(alphaParamName, alpha);
put(betaParamName, beta);
}};
}
/**
* Cannot use setters because of Number
*/
@Override
public void setParam(String paramName, Value value) {
if (paramName.equals(alphaParamName)) alpha = value;
else if (paramName.equals(betaParamName)) beta = value;
else throw new RuntimeException("Unrecognised parameter name: " + paramName);
super.setParam(paramName, value); // constructDistribution
}
private static final Double[] domainBounds = {0.0, 1.0};
public Double[] getDomainBounds() {
return domainBounds;
}
}